It was an unhappy return to an old stomping ground for ex-Victory pair Ernie Merrick and Carlos Hernandez, as the visitors from New Zealand found themselves 3-0 down within the first 31 minutes at Etihad Stadium.
The Kiwi side pulled a goal back in the first half and grabbed a second with five minutes remaining to set up a tense finish.
But Victory survived to record their second triumph in succession and join Western Sydney Wanderers on eight points after four rounds of the 2013-14 A-League season, one point behind leaders Brisbane Roar. Wellington are second from bottom, level on two points with Melbourne Heart.
Following a feisty start to the clash, Muscat's first in charge after succeeding the Socceroos-bound Ange Postecoglou, Victory opened the scoring in the ninth minute through Archie Thompson, who received a pass with his back to goal before turning and shooting beyond Glen Moss.
A handball from Thompson appeared to go unnoticed before he found the net, but the Phoenix had only themselves to blame when James Troisi capitalised on Andrew Durante's weak header back to his goalkeeper and made it 2-0.
Victory added a third in the 31st minute, Troisi producing an exquisite chipped finish following a precise pass from Kosta Barbarouses.
At that point the game looked dead and buried with an hour still to go, but six minutes later former Victory favourite Hernandez breathed life back into the contest when his slide-rule pass released Jeremy Brockie through on goal, and the New Zealand international made no mistake with a shot through Nathan Coe's legs.
The home side appeared comfortable for much of a tame second half, but Paul Ifill pulled another back late on as he cut in from the right flank and beat two defenders before poking home.
However, there was to be no dramatic escape act for Wellington and Merrick's search for a first victory in charge of his new club goes on.
